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core::scoring::carbon_hbonds::CarbonHBondPotential Class Reference

#include <CarbonHBondPotential.hh>

Inheritance diagram for core::scoring::carbon_hbonds::CarbonHBondPotential:
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Public Member Functions

 CarbonHBondPotential ()
 ctor, reads data file More...
 
Real get_potential (Size const &atom_type, Vector const &H_A_vector, Vector const &D_H_vector, Vector const &B_A_vector, bool calculate_deriv, Vector &deriv_vector) const
 Calculate chbond energies for non-rna atom pairs. More...
 
Real get_potential_RNA (Vector const &r_H_A, Vector const &z_i, bool const &update_deriv, Vector &deriv) const
 Calculate the rna-specific chbond energies. The derivative vector returned is the force vector on the acceptor atom. Multiply by -1 to get the force vector on the donor atom. More...
 
Real get_potential (Size const &atom_type, Vector const &H_A_vector, Vector const &D_H_vector, Vector const &B_A_vector) const
 second declaration to allow skipping deriv; gcc 4.1.3 does not like setting default parameters for a pass-by-reference parameter More...
 
Real max_dis () const
 

Private Member Functions

void read_potential ()
 

Private Attributes

Real bin_width_
 
Real max_dist_
 
Real const aroC_scale_factor_
 
Size const num_carbon_donor_atoms_
 
Size const num_bins_
 
utility::vector1
< ObjexxFCL::FArray1D< Real > > 
carbon_hbond_parameter_
 
utility::vector1< std::string > carbon_donors_
 
ObjexxFCL::FArray1D< Sizestandard_atomtype_to_carbon_donor_index_
 
Real const rna_cos_theta_cutoff_
 
Real const rna_cos_theta_fade_zone_
 
Real const rna_ch_o_bond_distance_
 

Constructor & Destructor Documentation

core::scoring::carbon_hbonds::CarbonHBondPotential::CarbonHBondPotential ( )

ctor, reads data file

ctor, reads data file. Need to configure to allow alternate tables/atom_sets

References read_potential().

Member Function Documentation

Real core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential ( Size const &  atom_type,
Vector const &  H_A_vector,
Vector const &  D_H_vector,
Vector const &  B_A_vector,
bool  calculate_deriv,
Vector deriv_vector 
) const
Real core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential ( Size const &  atom_type_index,
Vector const &  H_A_vector,
Vector const &  D_H_vector,
Vector const &  B_A_vector 
) const

second declaration to allow skipping deriv; gcc 4.1.3 does not like setting default parameters for a pass-by-reference parameter

Locally allocated deriv_vector is passed by reference into the more general implementation of the get_potential function; moreover, the calculate-derivative flag is set to false in that call. This is the "evaluate only the score" interface to the chbond potential.

References get_potential().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential_RNA ( Vector const &  r_H_A,
Vector const &  z_i,
bool const &  update_deriv,
Vector deriv 
) const

Calculate the rna-specific chbond energies. The derivative vector returned is the force vector on the acceptor atom. Multiply by -1 to get the force vector on the donor atom.

References core::scoring::rna::get_fade_correction(), max_dist_, rna_ch_o_bond_distance_, rna_cos_theta_cutoff_, rna_cos_theta_fade_zone_, and protocols::hybridization::score.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::max_dis ( ) const
inline

References max_dist_.

void core::scoring::carbon_hbonds::CarbonHBondPotential::read_potential ( )
private

Member Data Documentation

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::aroC_scale_factor_
private

Referenced by read_potential().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::bin_width_
private

Referenced by get_potential(), and read_potential().

utility::vector1< std::string > core::scoring::carbon_hbonds::CarbonHBondPotential::carbon_donors_
private

Referenced by read_potential().

utility::vector1< ObjexxFCL::FArray1D <Real> > core::scoring::carbon_hbonds::CarbonHBondPotential::carbon_hbond_parameter_
private

Referenced by get_potential(), and read_potential().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::max_dist_
private
Size const core::scoring::carbon_hbonds::CarbonHBondPotential::num_bins_
private

Referenced by read_potential().

Size const core::scoring::carbon_hbonds::CarbonHBondPotential::num_carbon_donor_atoms_
private

Referenced by read_potential().

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::rna_ch_o_bond_distance_
private

Referenced by get_potential_RNA().

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::rna_cos_theta_cutoff_
private

Referenced by get_potential_RNA().

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::rna_cos_theta_fade_zone_
private

Referenced by get_potential_RNA().

ObjexxFCL::FArray1D< Size > core::scoring::carbon_hbonds::CarbonHBondPotential::standard_atomtype_to_carbon_donor_index_
private

Referenced by get_potential(), and read_potential().


The documentation for this class was generated from the following files: